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[Display omitted] • The transcriptome and translatome of 8 tissues of cotton generated large datasets. • De novo transcriptome assembly and ribosome profiling fine-tune cotton genome annotation. • Unannotated translational events including sORFs (uORFs and dORF), and lncRNAs were identified. • Omics integrated analysis of normal fiber ZM24 and short fiber pag1 explored fiber-specific genes. • GhKCS6 overexpression showed greater fiber length than the control and validated our approach. The unavailability of intergenic region annotation in whole genome sequencing and pan-genomics hinders efforts to enhance crop improvement. Despite advances in research, the impact of post-transcriptional regulation on fiber development and translatome profiling at different stages of fiber growth in cotton (G. hirsutum) remains unexplored. We utilized a combination of reference-guided de novo transcriptome assembly and ribosome profiling techniques to uncover the hidden mechanisms of translational control in eight distinct tissues of upland cotton. Our study identified P-site distribution at three-nucleotide periodicity and dominant ribosome footprint at 27 nucleotides. Specifically, we have detected 1,589 small open reading frames (sORFs), including 1,376 upstream ORFs (uORFs) and 213 downstream ORFs (dORFs), as well as 552 long non-coding RNAs (lncRNAs) with potential coding functions, which fine-tune the annotation of the cotton genome. Further, we have identified novel genes and lncRNAs with strong translation efficiency (TE), while sORFs were found to affect mRNA transcription levels during fiber elongation. The reliability of these findings was confirmed by the high consistency in correlation and synergetic fold change between RNA-sequencing (RNA-seq) and Ribosome-sequencing (Ribo-seq) analyses. Additionally, integrated omics analysis of the normal fiber ZM24 and short fiber pag1 cotton mutant revealed several differentially expressed genes (DEGs), and fiber-specific expressed (high/low) genes associated with sORFs (uORFs and dORFs). These findings were further supported by the overexpression and knockdown of GhKCS6 , a gene associated with sORFs in cotton, and demonstrated the potential regulation of the mechanism governing fiber elongation on both the transcriptional and post-transcriptional levels. Reference-guided transcriptome assembly and the identification of novel transcripts fine-tune the annotation of the cotton genome and predicted the landscape of fiber development. Our approach provided a high-throughput method, based on multi-omics, for discovering unannotated ORFs, hidden translational control, and complex regulatory mechanisms in crop plants. [ABSTRACT FROM AUTHOR]

[Display omitted] • Provide chromosome-level genome assemblies for BP (Boleophthalmus pectinirostris) and PM (Periophthalmus magnuspinnatus). • Confirm two specific chromosome fission events in the PM genome by synteny comparison and ancestral chromosome reconstruction. • Reveal molecular clues from the loss of some important genes (such as SCPP and aanat1a) in certain or all of the three mudskippers for the water-to-land adaptation. Mudskippers are a large group of amphibious fishes that have developed many morphological and physiological capacities to live on land. Genomics comparisons of chromosome-level genome assemblies of three representative mudskippers, Boleophthalmus pectinirostris (BP), Periophthalmus magnuspinnatus (PM) and P. modestus (PMO), may be able to provide novel insights into the water-to-land evolution and adaptation. Two chromosome-level genome assemblies for BP and PM were respectively sequenced by an integration of PacBio, Nanopore and Hi-C sequencing. A series of standard assembly and annotation pipelines were subsequently performed for both mudskippers. We also re-annotated the PMO genome, downloaded from NCBI, to obtain a redundancy-reduced annotation. Three-way comparative analyses of the three mudskipper genomes in a large scale were carried out to discover detailed genomic differences, such as different gene sizes, and potential chromosomal fission and fusion events. Comparisons of several representative gene families among the three amphibious mudskippers and some other teleosts were also performed to find some molecular clues for terrestrial adaptation. We obtained two high-quality haplotype genome assemblies with 23 and 25 chromosomes for BP and PM respectively. We also found two specific chromosome fission events in PM. Ancestor chromosome analysis has discovered a common fusion event in mudskipper ancestor. This fusion was then retained in all the three mudskipper species. A loss of some SCPP (secretory calcium-binding phosphoprotein) genes were identified in the three mudskipper genomes, which could lead to reduction of scales for a part-time terrestrial residence. The loss of aanat1a gene, encoding an important enzyme (arylalkylamine N-acetyltransferase 1a, AANAT1a) for dopamine metabolism and melatonin biosynthesis, was confirmed in PM but not in PMO (as previously reported existence in BP), suggesting a better air vision of PM than both PMO and BP. Such a tiny variation within the genus Periophthalmus exemplifies to prove a step-by-step evolution for the mudskippers' water-to-land adaptation. These high-quality mudskipper genome assemblies will become valuable genetic resources for in-depth discovery of genomic evolution for the terrestrial adaptation of amphibious fishes. [ABSTRACT FROM AUTHOR]

[Display omitted] • We present a chromosome-scale genome assembly for the canine heartworm Dirofilaria immitis. • Comparative analyses with filarial nematodes reveal sex-linked and autosomal chromosomes, and chromosomal rearrangements. • Population genetics of diverse isolates shows broad genetic structure, but differences in diversity between regions. • Previously proposed variants associated with macrocyclic lactone resistance form two discrete clusters on chromosome 3. The heartworm, Dirofilaria immitis, is a filarial parasitic nematode responsible for significant morbidity and mortality in wild and domesticated canids. Resistance to macrocyclic lactone drug prevention represents a significant threat to parasite control and has prompted investigations to understand the genetic determinants of resistance. This study aimed to improve the genomic resources of D. immitis to enable a more precise understanding of how genetic variation is distributed within and between parasite populations worldwide, which will inform the likelihood and rate by which parasites, and in turn, resistant alleles, might spread. We have guided the scaffolding of a recently published genome assembly for D. immitis (ICBAS_JMDir_1.0) using the chromosomal-scale reference genomes of Brugia malayi and Onchocerca volvulus, resulting in an 89.5 Mb assembly composed of four autosomal- and one sex-linked chromosomal-scale scaffolds representing 99.7% of the genome. Publicly available and new whole-genome sequencing data from 32 D. immitis samples from Australia, Italy and the USA were assessed using principal component analysis, nucleotide diversity (Pi) and absolute genetic divergence (Dxy) to characterise the global genetic structure and measure within- and between-population diversity. These population genetic analyses revealed broad-scale genetic structure among globally diverse samples and differences in genetic diversity between populations; however, fine-scale subpopulation analysis was limited and biased by differences between sample types. Finally, we mapped single nucleotide polymorphisms previously associated with macrocyclic lactone resistance in the new genome assembly, revealing the physical linkage of high-priority variants on chromosome 3, and determined their frequency in the studied populations. This new chromosomal assembly for D. immitis now allows for a more precise investigation of selection on genome-wide genetic variation and will enhance our understanding of parasite transmission and the spread of genetic variants responsible for resistance to treatment. [ABSTRACT FROM AUTHOR]

A marine red yeast, Rhodosporidium sphaerocarpum , is generally used for the production of lipids and carotenoids. In a previous study, we demonstrated that a marine-derived R. sphaerocarpum GDMCC 60679 can efficiently remove ammonia nitrogen and exhibit multiple probiotic functions for shrimp, Litopenaeus vannamei. Here, we performed a genome assembly of the strain GDMCC 60679 using a combination of the data from Illumina PE and PacBio CLR reads. The genome has a size of 18.03 Mb and consists of 32 contigs with an N50 length of 1,074,774 bp and GC content of 63 %. The genome was predicted to contain 6092 protein-coding genes, 5962 of which were functionally annotated. Metabolic pathways responsible for the ammonia assimilation and the synthesis of lipids and carotenoids were particularly examined to explore and characterize genes contributing to these functions. Whole-genome sequence and annotation of the strain lays a foundation to reveal the molecular mechanism of its prominent biological functions and will facilitate us to further expand new applications of yeasts in Rhodosporidium. [ABSTRACT FROM AUTHOR]

[Display omitted] • Genome skimming has been used to characterise helminths from human and livestock faeces. • The approach showed good specificity but low sensitivity relative to quantitative PCR diagnostics. • Ascaris mitochondrial genomes can be phylogenetically resolved among global isolates. • Challenges include cost, process optimisation, adequate sequencing infrastructure and quality reference genomes. The identification of gastrointestinal helminth infections of humans and livestock almost exclusively relies on the detection of eggs or larvae in faeces, followed by manual counting and morphological characterisation to differentiate species using microscopy-based techniques. However, molecular approaches based on the detection and quantification of parasite DNA are becoming more prevalent, increasing the sensitivity, specificity and throughput of diagnostic assays. High-throughput sequencing, from single PCR targets through to the analysis of whole genomes, offers significant promise towards providing information-rich data that may add value beyond traditional and conventional molecular approaches; however, thus far, its utility has not been fully explored to detect helminths in faecal samples. In this study, low-depth whole genome sequencing, i.e. genome skimming, has been applied to detect and characterise helminth diversity in a set of helminth-infected human and livestock faecal material. The strengths and limitations of this approach are evaluated using three methods to characterise and differentiate metagenomic sequencing data based on (i) mapping to whole mitochondrial genomes, (ii) whole genome assemblies, and (iii) a comprehensive internal transcribed spacer 2 (ITS2) database, together with validation using quantitative PCR (qPCR). Our analyses suggest that genome skimming can successfully identify most single and multi-species infections reported by qPCR and can provide sufficient coverage within some samples to resolve consensus mitochondrial genomes, thus facilitating phylogenetic analyses of selected genera, e.g. Ascaris spp. Key to this approach is both the availability and integrity of helminth reference genomes, some of which are currently contaminated with bacterial and host sequences. The success of genome skimming of faecal DNA is dependent on the availability of vouchered sequences of helminths spanning both taxonomic and geographic diversity, together with methods to detect or amplify minute quantities of parasite nucleic acids in mixed samples. [ABSTRACT FROM AUTHOR]

• Not all genomic regions and lengths of hepatitis E virus (HEV) are equally suited for use in genetic analyses. • Generally, longer nucleic acid stretches yield better accuracy in predicting the viral subtype. • Analysis of molecular and epidemiological data of HEV in the Netherlands indicates the ability of the 493 nt fragment to detect short term changes in the viral population size. • In the absence of whole genome sequences the 493 bp fragment can be used for molecular typing and population structure characterization of HEV. The aim of this study was to investigate to what extent fragments of the HEV genome could be used for accurate diagnostics and inference of viral population-scale processes. For this, we selected all the published whole genome sequences from the NCBI GenBank and trimmed them to various fragment lengths (ORF1,2,3, ORF1, ORF2, ORF3, 493 nt in ORF2 and 148 nt in ORF2). Each of the fragment lengths was used to infer the richness and diversity of the viral sequence types, typing accuracy, and potential use in phylodynamics. The results obtained from the different fragments were compared. We observed that, generally, the longer the nucleic acid fragment used in typing, the better the accuracy in predicting the viral subtype. However, the dominant HEV subtypes circulating in Europe were relatively well classified even by the 493 nt fragment, with false negative rates as low as 8 in 1000 typed sequences. Most fragments also give comparable results in analyses of population size, albeit with shorter fragments showing a broader 95 % highest posterior density interval and less obvious increase of the viral effective population size. The reconstructed phylogenies of a heterochronous subset indicated a good concordance between all the fragments, with the major clades following similar branching patterns. Furthermore, we have used the HEV sequence data from the Netherlands available in the HEVnet database as a case study for reconstruction of population size changes in the past decades. This data showed that molecular and epidemiological results are concordant and point to an increase in the viral effective population size underlying the observed increase in incidence of acute HEV infection cases. In the absence of whole genome sequencing data, the 493 bp fragment can be used for analyzing HEV strains currently circulating in Europe, as it is informative for describing short term population-scale processes. [ABSTRACT FROM AUTHOR]

Understanding the prevalence and distribution of CRISPR-Cas systems across different strains can illuminate the ecological and evolutionary dynamics of Clostridium botulinum populations. In this study, we conducted genome mining to characterize the CRISPR-Cas systems of C. botulinum strains. Our analysis involved retrieving complete genome sequences of these strains and assessing the diversity, prevalence, and evolution of their CRISPR-Cas systems. Subsequently, we performed an analysis of homology in spacer sequences from identified CRISPR arrays to investigate and characterize the range of targeted phages and plasmids. Additionally, we investigated the evolutionary trajectory of C. botulinum strains under selective pressures from foreign invasive DNA. Our findings revealed that 306 strains possessed complete CRISPR-Cas structures, comprising 58% of the studied C. botulinum strains. Secondary structure prediction of consensus repeats indicated that subtype II-C, with longer stems compared to subtypes I D and I B, tended to form more stable RNA secondary structures. Moreover, protospacer motif analysis demonstrated that strains with subtype I B CRISPR-Cas systems exhibited 5′-CGG-3′, 5′-CC-3′, and 5′-CAT-3′ motifs in the 3′ flanking regions of protospacers. The diversity observed in CRISPR-Cas systems indicated their classification into subtypes I B, I D, II-C, III-B, and III-D. Furthermore, our results showed that systems with subtype I D and III-D frequently harbored similar spacer patterns. Moreover, analysis of spacer sequences homology with phage and prophage genomes highlighted the specific activities exhibited by subtype I B and III-B against phages and plasmids, providing valuable insights into the functional specialization within these systems. • There is great diversity between the CRISPR-Cas systems identified in Clostridium botulinum strains. • Results indicated that some specific groups of plasmids were targeted with specific CRISPR array systems. • Spacers of strains which harbored CRISPR-Cas subtypes I B and III-B, targeted more diversity of foreign phages. • CRISPR system is naturally active and important in terms of adaptive immunity and evolutionary relationship. [ABSTRACT FROM AUTHOR]

[Display omitted] • Delta to Omicron shift indicates COVID-19′s evolving landscape. • Predominant clade and lineage identified as 21A and B.1.617.2 respectively. • Major Spike mutations identified are T19R, K77T, G142D, T478K, L452R, E156G. • Monitoring SARS-CoV-2 evolution is vital to enhance preventive strategies. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to challenge the global healthcare with emerging variants and higher infectivity as well as morbidities. This study investigated potential age-related variations through genomic characterization of the virus under common clinical settings. A cohort comprising 71 SARS-CoV-2 strains from both infected infants and accompanying adults, diagnosed via RT-PCR at a tertiary pediatric hospital and research center, underwent Illumina paired-end sequencing. The subsequent analysis involved standard genomic screening, phylogeny construction, and mutational analyses. The analyzed SARSCoV- 2 strains were compared with globally circulating variants. The overall distribution revealed 67.61 % Delta, 25.7 % Omicron, and 1 % either Kappa or Alpha variants. In 2021, Delta predominated at ∼ 94 %, with Alpha/Kappa accounting for around 5 %. However, in 2022, over 94 % of the samples were Omicron variants, signifying a substantial shift from Delta dominance. Delta variants constituted 69.5 % of infections in adults and 78.5 % in infants, while Omicron variants were responsible for 31 % of cases in infants and 18 % in adults. The Spike region harbored the majority of mutations, with T19R being the most prevalent mutation in the Delta lineage. Notably, the frequencies of this mutation varied between infants and adults. In Omicron samples, G142D emerged as the most prevalent mutation. Our dataset predominantly featured clade 21A and lineage B.1.617.2. This study underscores the differential clinical presentations and genomic characteristics of SARS-CoV-2 in pediatric patients and accompanying adults. Understanding the dynamic evolution of the SARS- CoV-2 in both pediatric and adults can help in strengthening prophylactic measures. [ABSTRACT FROM AUTHOR]

Spreading of Mycobacterium bovis causing animal tuberculosis (TB) at livestock-wildlife-environment interfaces remains a significant problem. Recently, we provided evidence of widespread environmental contamination of an endemic animal TB setting with viable and dormant M. bovis cells able to recover metabolic activity, making indirect transmission via environmental contamination plausible. We now report the first whole genome sequences of M. bovis recovered from the environment. We establish epidemiological links at the environment-animal interface by phylogenomic comparison of these M. bovis genomes with those isolated from livestock and wild ungulates from the same area. Environmental and animal genomes are highly intertwined and distribute similarly into the same M. bovis lineages, supporting several instances of environmental contamination. This study provides compelling evidence of M. bovis excretion into the environment and viability maintenance, supporting the environment as a potential source of new infection. These insights have clear implications for policy formulation, advocating environmental surveillance and an ecosystem perspective in TB control programs. We report the first whole genome sequences of M. bovis from the environment and establish epidemiological links at the environment-animal interface, demonstrating close phylogenomic relatedness of animal and environmental M. bovis. Definitive evidence of M. bovis excretion into the environment with viability maintenance is provided, supporting the environment as a potential source of new infection. Implications of this work include methodological innovations offering a tool to resolve indirect transmission chains and support customized biosecurity measures. Policy formulation aiming at the control of animal tuberculosis and cost mitigation should consider these findings, encouraging environmental surveillance in official eradication programmes. [Display omitted] • M. bovis shed from TB-infected animals may remain viable in the environment. • Whole genome sequencing of environmental M. bovis is reported for the first time. • M. bovis lineages distribute similarly at the animal-environment interface. • Environmental and animal M. bovis genomes are phylogenetically highly intertwined. • The environment is a potential source of new infections in animal TB endemic areas. [ABSTRACT FROM AUTHOR]

• The two CnmeGV isolates came from the same region and were collected 35 years apart. • CnmeGV hr4 presents a nested repeating pattern. • Tandem repeats were the only highly variable region of CnmeGV during replication. • CnmeGV obtained a non-coding sequence from its host. Cnaphalocrocis medinalis granulovirus (CnmeGV), belonging to Betabaculovirus cnamedinalis , can infect the rice pest, the rice leaf roller. In 1979, a CnmeGV isolate, CnmeGV-EP, was collected from Enping County, China. In 2014, we collected another CnmeGV isolate, CnmeGV-EPDH3, at the same location and obtained the complete virus genome sequence using Illumina and ONT sequencing technologies. By combining these two virus isolates, we updated the genome annotation of CnmeGV and conducted an in-depth analysis of its genome features. CnmeGV genome contains abundant tandem repeat sequences, and the repeating units in the homologous regions (hrs) exhibit overlapping and nested patterns. The genetic variations within EPDH3 population show the high stability of CnmeGV genome, and tandem repeats are the only region of high genetic variation in CnmeGV genome replication. Some defective viral genomes formed by recombination were found within the population. Comparison analysis of the two virus isolates collected from Enping showed that the proteins encoded by the CnmeGV-specific genes were less conserved relative to the baculovirus core genes. At the genomic level, there are a large number of SNPs and InDels between the two virus isolates, especially in and around the bro genes and hrs. Additionally, we discovered that CnmeGV acquired a segment of non-ORF sequence from its host, which does not provide any new proteins but rather serves as redundant genetic material integrated into the viral genome. Furthermore, we observed that the host's transposon piggyBac has inserted into some virus genes. Together, dsDNA viruses could acquire non-coding genetic material from their hosts to expand the size of their genomes. These findings provide new insights into the evolution of dsDNA viruses. [ABSTRACT FROM AUTHOR]

Aeromonas veronii , a significant pathogen in aquatic environments, poses a substantial threat to both human and animal health, particularly in aquaculture. In this study, we isolated A. veronii strain GD2019 from diseased largemouth bass (Micropterus salmoides) during a severe outbreak of aeromonad septicemia in Guangdong Province, China. The complete genome sequence of A. veronii GD2019 revealed that GD2019 contains a single chromosome of 4703,168 bp with an average G+C content of 58.3 %. Phylogenetic analyses indicated that GD2019 forms a separate sub-branch in A. veronii and comparative genomic analyses identified the existence of an intact Type III secretion system. Moreover, to investigate the genes that are required for the conditional fitness of A. veronii under various stresses, a high-density transposon insertion library in GD2019 was generated by a Tn5-based transposon and covers 6311 genomic loci including 4155 genes and 2156 intergenic regions. Leveraging this library, 630 genes were classified as essential genes for growth in rich-nutrient LB medium. Furthermore, the genes GE001863/NtrC and GE002550 were found to confer tolerance to sodium hypochlorite in A. veronii. GE002562 and GE002614 were associated with the resistance to carbenicillin. Collectively, our results provide abundant genetic information on A. veronii , shedding light on the pathogenetic mechanisms of Aeromonas. [ABSTRACT FROM AUTHOR]

Advances in next-generation sequencing (NGS) have significantly reduced the cost and improved the efficiency of obtaining single nucleotide polymorphism (SNP) markers, particularly through restriction site-associated DNA sequencing (RAD-seq). Meanwhile, the progression in whole genome sequencing has led to the utilization of an increasing number of reference genomes in SNP calling processes. This study utilized RAD-seq data from 242 individuals of Engelhardia roxburghiana , a tropical tree of the walnut family (Juglandaceae), with SNP calling conducted using the STACKS pipeline. We aimed to compare both reference-based approaches, namely, employing a closely related species as the reference genome versus the species itself as the reference genome, to evaluate their respective merits and limitations. Our findings indicate a substantial discrepancy in the number of obtained SNPs between using a closely related species as opposed to the species itself as reference genomes, the former yielded approximately an order of magnitude fewer SNPs compared to the latter. While the missing rate of individuals and sites of the final SNPs obtained in the two scenarios showed no significant difference. The results showed that using the reference genome of the species itself tends to be prioritized in RAD-seq studies. However, if this is unavailable, considering closely related genomes is feasible due to their wide applicability and low missing rate as alternatives. This study contributes to enrich the understanding of the impact of SNP acquisition when utilizing different reference genomes. • This study contributes to enrich the knowledge concerning the influence of SNP acquisition when employing different reference genomes. • The SNP counts vary based on the choice of reference genomes, with using the species itself yielding optimal results for SNP calling. • Whole-genome sequencing is called for to obtain more accurate results. [ABSTRACT FROM AUTHOR]

• TaqMan assay targeting spike Δ69-70, G339D, and Q493R distinguishes Omicron variants • Omicron sublineage results from of whole genome sequencing and TaqMan assay were highly consistent • In samples mutated with the TaqMan probe, the results need to be visually confirmed Recently, the Omicron strain of SARS-CoV-2 has spread and replaced the previously dominant Delta strain. Several Omicron sublineages (BA.1, BA.1.1, and BA.2) have been identified, with in vitro and preclinical reports showing that the pathogenicity and therapeutic efficacy differs between BA.1 and BA.2. We sought to develop a TaqMan assay to identify these subvariants. A TaqMan assay was constructed for rapid identification and genotyping of Omicron sublineages with 171 samples. We analyzed three characteristic mutations of the spike gene, Δ69–70, G339D, and Q493R, by TaqMan assay. The accuracy of the TaqMan assay was examined by comparing its results with the results of whole genome sequencing (WGS) analysis. A total of 171 SARS-CoV-2 positive samples were analyzed by WGS and TaqMan assay. The 127 samples determined as BA.1/BA.1.1 by WGS were all positive for Δ69–70, G339D and Q493R by TaqMan assay. A total of 42 samples, determined as BA.2 by WGS, were negative for Δ69–70 but positive for G339D and Q493R by TaqMan. Two samples with G339N were determined to be inconclusive by the TaqMan method. Except for these two samples, the concordance rate between WGS and the TaqMan assay was 100% (169/169). TaqMan assays targeting characteristic mutations are useful for identification and discrimination of Omicron sublineages. [ABSTRACT FROM AUTHOR]

Over the past quarter-century, the field of evolutionary biology has been transformed by the emergence of complete genome sequences and the conceptual framework known as the 'Net of Life.' This paradigm shift challenges traditional notions of evolution as a tree-like process, emphasizing the complex, interconnected network of gene flow that may blur the boundaries between distinct lineages. In this context, gene loss, rather than horizontal gene transfer, is the primary driver of gene content, with vertical inheritance playing a principal role. The 'Net of Life' not only impacts our understanding of genome evolution but also has profound implications for classification systems, the rapid appearance of new traits, and the spread of diseases. Here, we explore the core tenets of the 'Net of Life' and its implications for genome-scale phylogenetic divergence, providing a comprehensive framework for further investigations in evolutionary biology. [ABSTRACT FROM AUTHOR]

• Dolichospermum akinetes isolated from a 10cm sediment core represent a 45-year history. • Samples with 10 akinete cells produced near complete genomes using single-cell genome amplification. • Lake Stechlin akinete genomes were very similar over the 45 year history. • SNP analysis revealed two populations that changed dominance with environmental conditions. Dolichospermum is a cyanobacterial genus commonly associated with toxic blooms in lakes and brackish water bodies worldwide, and is a long-term resident of Lake Stechlin, northeastern Germany. In recent decades, shifts in the phosphorus loading and phytoplankton species composition have seen increased biomass of Dolichospermum during summer blooms from 1998, peaking around 2005, and declining after 2020. Cyanobacteria are known to rapidly adapt to new environments, facilitated by genome adaptation. To investigate the changes in genomic features that may have occurred in Lake Stechlin Dolichospermum during this time of increased phosphorus loading and higher biomass, whole genome sequence analysis was performed on samples of ten akinetes isolated from ten, 1 cm segments of a sediment core, representing a ∼45-year period from 1970 to 2017. Comparison of these genomes with genomes of extant isolates revealed a clade of Dolichospermum that clustered with the ADA-6 genus complex, with remarkable genome stability, without gene gain or loss events in response to recent environmental changes. The genome characteristics indicate that this species is suited to a deep-chlorophyll maximum, including additional light-harvesting and phosphorus scavenging genes. Population SNP analysis revealed two sub-populations that shifted in dominance as the lake transitioned between oligotrophic and eutrophic conditions. Overall, the results show little change within the population, despite diversity between extant populations from different geographic locations and the in-lake changes in phosphorus concentrations. [ABSTRACT FROM AUTHOR]

• In a patient with mitochondrial disorder, compound heterozygous deletion with an overlapping region of ∼142 kb encompassing NDUFAF2 and ERCC8 genes was identified. • Mitochondrial dysfunction was observed in fetal-derived fibroblasts harboring the contiguous gene deletion. • Custom MLPA-based assay was developed to screen the identified deletion in the extended family of the proband. Genomic investigations on an infant who presented with a putative mitochondrial disorder led to identification of compound heterozygous deletion with an overlapping region of ∼142 kb encompassing two nuclear encoded genes namely ERCC8 and NDUFAF2. Investigations on fetal-derived fibroblast culture demonstrated impaired bioenergetics and mitochondrial dysfunction, which explains the phenotype and observed infant mortality in the present study. The genetic findings from this study extended the utility of whole-genome sequencing as it led to development of a MLPA-based assay for carrier screening in the extended family and the prenatal testing aiding in the birth of two healthy children. [ABSTRACT FROM AUTHOR]

Sophora koreensis Nakai, an endemic species distributed only in the Korean Peninsula, is of great geographical, economic, and taxonomic importance. Although its complete chloroplast (cp) genome sequence has been reported, its mitochondrial (mt) genome sequence has not yet been studied. Therefore, in this study, we aimed to investigate its mt genome sequence and compare it with those reported for other Fabaceae species. Total genomic DNA was extracted from fresh S. koreensis leaves collected from natural habitats in Gangwon-do Province, South Korea. This was followed by polymerase chain reaction (PCR) amplification of cpDNA insertions in the mt genome and the detection of microsatellites and dispersed repeats in the cp and mt genomes. Finally, the cp and mt genomes of S. koreensis were compared with those reported for other Fabaceae species. The cp sequence of S. koreensis showed identical gene orders and contents as those previously reported. Only six substitutions and one deletion were detected with 99 % homology. Conversely, the complete mt genome sequence, which was 517,845 bp in length and encoded 61 genes, including 43 protein-coding, 15 transfer RNAs, and 3 ribosomal RNA genes, was considerably different from that of S. japonica in terms of gene order and composition. Further, the mt genome of S. koreensis included ca. 7 and 3 kb insertions, representing an intracellular gene transfer (IGT) event, and the regions with these insertions were determined to be originally present in the cp genome. This IGT event was also confirmed via PCR amplification. IGT events can be induced via biological gene expression control or the use of repetitive sequences, and they provide important insights into the evolutionary lineage of S. koreensis. However, further studies are needed to clarify the gene transfer mechanisms between the two organelles. [ABSTRACT FROM AUTHOR]

Decapod hepandensovirus 1 (DHPV) is a viral pathogen that causes growth retardation and decreased feed conversion efficiency in penaeid shrimp. The virus exhibits high genetic variation between different hosts and geographical locations. It has been primarily reported in cultured Penaeus monodon , P. chinensis , and P. merguiensis , and a new type of DHPV has recently been reported in P. vannamei cultured in Korea and Taiwan. In this study, the genome of a recently reported new type of DHPV was fully sequenced by conventional Sanger sequencing combined with a next-generation sequencing approach. Similar to the other types of DHPVs infecting several shrimp species other than P. vannamei , a new type of DHPV contained a linear, single-stranded DNA genome of 6173 bp comprising three major open reading frames. However, by detailed comparative genome and phylogenetic analysis, the virus was not clustered with the pre-existing genotypes, suggesting the emergence of a possible novel genotype of DHPV in cultured shrimps. This study is the first to report the complete genomic sequence of DHPV identified in P. vannamei. • A new genotype of Decapod hepandensovirus 1 (DHPV) is found in Penaeus vannamei. • Complete genome sequence of DHPV infecting Penaeus vannamei presented in the study. • The DNA genome is 6173 bp in size, comprising 3 major open reading frames (ORFs). • ORF 3 region of the new DHPV shows notably low similarity to 9 historic viruses. • The phylogenetic tree shows the new DHPV doesn't cluster with existing genotypes. [ABSTRACT FROM AUTHOR]

• The study is the first comprehensive molecular atlas for primary GCOC. • Alterations in the 22q11.21 region is a novel discovery of pathogenesis. • Cytokine-cytokine receptor interaction and PI3K-Akt signaling pathway could be the underlying oncogenesis of GCOC. There is currently no comprehensive genome-wide description of the primary ghost cell odontogenic carcinoma (GCOC), hindering our understanding of pathogenesis. We herein present a case with comprehensive clinical, genome and transcriptomic analysis. These will serve as the first comprehensive molecular atlas for primary GCOC. A 58-year-old male underwent subtotal resection with prosthetic restoration. Genome sequencing (WGS) detected previously identified CTNNB1 mutation with novel alterations of MAP3K, EP300, and 22q11.21 region. Transcriptome results showed significant involvement of cytokine-cytokine receptor interaction and PI3K-Akt signaling pathway. These results need to be compared with more GCOCs for more accurate clinical guidance. [ABSTRACT FROM AUTHOR]

The University of the Free State - Next Generation Sequencing (NGS) Unit, Bloemfontein, South Africa, hosted a data and bioinformatics workshop from 19 to 22 June 2018. The workshop was coordinated by the African Enteric Viruses Genome Initiative (AEVGI) with support from the Bill & Melinda Gates Foundation. The event introduced technologies in NGS and data analysis with focus on the rotavirus (RV) genome. The workshop fostered interactions and networking between professionals, scientific experts, technicians and students. The courses provided an overview of RV diarrhoea and its burden in Africa, while highlighting the key resources and methodologies in NGS and advanced bioinformatics in deciphering vaccine impact. It was concluded that, despite the reported significant decline in RV associated-diarrhoea mortality and morbidity in Africa due to RV vaccine impact, the need for continuous surveillance and genomic characterization to better understand the ever-changing dynamics of RV strains is imperative. [ABSTRACT FROM AUTHOR]

Direct-to-consumer (DTC) commercial companies offer genetic tests that are presented as allowing individuals the opportunity to increase their capacities to be in charge of their own healthcare managements. DTC companies deny performing medical tests, yet they provide data based on sequencing multigene panel or whole exome. This contradiction allows these companies to escape the requirements of a regulated medical practice that guarantees the quality of the tests, as well as the information and support for tested individuals. Herein, we illustrate the lack of such requirements by analysing the bad experience of a young man who dealt with DTC health genetic testing companies. There is an emergency for DTC testing to be either deprived of any medically relevant information, or carried out in a legally regulated medical framework. • By blurring the lines between commercial 'health' products and medical information, direct-to-consumer (DTC) companies are de facto performing medical tests. • Health professionals and the general population need to be aware of the significant limitations of DTC genetic health tests. • No medical decision should be taken on the basis of genetic results obtained outside of a legally regulated framework. • If DTC companies perform medical tests, they have to be carried out in a regulated framework guaranteeing their quality. [ABSTRACT FROM AUTHOR]

• WGS identified multidrug resistant Enterobacteriaceae in piggery waste. • Identified the last resort antibiotic resistant genes carrying bacterial plasmids. • Beta lactam resistant gene-specific PCR was used to validate the ARGs. The growing use of antibiotics in livestock is one of the main causes of the rapid global spread of antimicrobial resistance (AMR). However, extensive research on AMR in animals is currently absent. In this article, we provide the bacterial antibiotic resistance genes (ARGs) from piggery waste samples in West Bengal, India, based on whole genome sequencing (WGS). According to the study, there are alarmingly high levels of Enterobacteriaceae in piggery waste, especially slaughterhouse waste, that are resistant to beta-lactam, aminoglycoside, sulphonamide, and tetracycline. We found several plasmids carrying multidrug-resistant Enterobacteriaceae including resistant to last-resort medications like colistin and carbapenems. Our findings will serve as a guide for developing AMR management policies for livestock in India and aid in understanding the current AMR profiles of pigs. To grasp the actual situation with AMR in the pig sector, large scale sample screening must be done. [ABSTRACT FROM AUTHOR]

Equid gammaherpesvirus 5 (EHV5) is closely related to equid gammaherpesvirus 2 (EHV2). Detection of EHV5 is frequent in horse populations worldwide, but it is often without a clear and significant clinical impact. Infection in horses can often present as subclinical disease; however, it has been associated with respiratory disease, including equine multinodular pulmonary fibrosis (EMPF). Genetic heterogeneity within small regions of the EHV5 glycoprotein B (gB) sequences have been reported and multiple genotypes of this virus have been identified within individual horses, but full genome sequence data for these viruses is limited. The primary focus of this study was to assess the genomic diversity and natural recombination among EHV5 isolates. The genome size of EHV5 prototype strain and the five EHV5 isolates cultured for this study, including four isolates from the same horse, ranged from 181,929 to 183,428 base pairs (bp), with the sizes of terminal repeat regions varying from 0 to 10 bp. The nucleotide sequence identity between the six EHV5 genomes ranged from 95.5 to 99.1%, and the estimated average nucleotide diversity between isolates was 1%. Individual genes displayed varying levels of nucleotide diversity that ranged from 0 to 19%. The analysis of nonsynonymous substitution (Ka > 0.025) revealed high diversity in eight genes. Genome analysis using RDP4 and SplitsTree programs detected evidence of past recombination events between EHV5 isolates. Genomic diversity and recombination hotspots were identified among EHV5 strains. Recombination can drive genetic diversity, particularly in viruses that have a low rate of nucleotide substitutions. Therefore, the results from this study suggest that recombination is an important contributing factor to EHV5 genomic diversity. The findings from this study provide additional insights into the genetic heterogeneity of the EHV5 genome. • Considerable genomic diversity exist between EHV5 isolates, and higher among EHV5 isolates from different horses. • EHV5 genes including ORF73, gp350, gp42 and gH displayed high genetic heterogeneity marked by positive selection. • A larger proportion of EHV5 genes are seemingly undergoing purifying selection. • Evidence of recombination was detected among the EHV5 isolates examined. • Recombination may be an important mechanism driving EHV5 genome diversity. [ABSTRACT FROM AUTHOR]

Human rotavirus strains having the unconventional G3P[6] genotype have been sporadically detected in diarrheic patients in different parts of the world. However, the full genomes of only three human G3P[6] strains from Asian countries (China, Indonesia, and Vietnam) have been sequenced and characterized, and thus the exact origin and evolution of G3P[6] strains in Asia remain to be elucidated. Here, we sequenced and characterized the full genome of a G3P[6] strain (RVA/Human-wt/JPN/SO1199/2020/G3P[6]) found in a stool sample from a 3-month-old infant admitted with acute gastroenteritis in Japan. On full genomic analysis, strain SO1199 was revealed to have a unique Wa-like genogroup configuration: G3-P[6]-I5-R1-C1-M1-A8-N1-T1-E1-H1. VP6 genotype I5 and NSP1 genotype A8 are commonly found in porcine rotavirus strains. Furthermore, phylogenetic analysis demonstrated that all 11 genes of strain SO1199 were closely related to those of porcine and/or porcine-like human rotaviruses and thus appeared to be of porcine origin. Thus, strain SO1199 was shown to possess a porcine-like genomic backbone and thus is likely to be the result of interspecies transmission of a porcine rotavirus strain. Of note is that all 11 genes of strain SO1199 were phylogenetically located in clusters, distinct from those of the previously identified porcine-like human G3P[6] strains from around the world including Asia, suggesting the occurrence of independent porcine-to-human zoonotic transmission events. To our knowledge, this is the first report on full genome-based characterization of a human G3P[6] strain that has emerged in Japan. Our findings revealed the diversity of unconventional human G3P[6] strains in Asia, and provide important insights into the origin and evolution of G3P[6] strains. • Characterization of an unconventional human G3P[6] strain detected in Japan. • This is the first Japanese G3P[6] strain whose full genome has been characterized. • All 11 genes of the G3P[6] strain appeared to be of porcine origin. • Evidence for porcine-to-human interspecies transmission of rotaviruses. • There is diversity of zoonotic G3P[6] strains in Asia. [ABSTRACT FROM AUTHOR]

In 2018, a T. asinigenitalis strain (MCE663) was isolated in a Persian onager tested for contagious equine metritis (CEM) in a United Kingdom (UK) zoo. This bacterium had never been reported in the UK and Multilocus Sequence Typing described a new atypically divergent ST (ST60). Although the causative agent of CEM is the bacterium Taylorella equigenitalis , a first natural outbreak of endometritis caused by T. asinigenitalis ST70 was reported in 2019, putting its pathogenic potential into question. In this context, we aimed to further sequence the T. asinigenitalis MCE663 genome and characterize the strain using phenotypical and genetic approaches. Results showed that it gathered all identification characteristics of T. asinigenitalis with smaller colonies and it was susceptible to all tested antibiotics. Genome-level phylogeny showed that the genome MCE663 formed a distinct phylogroup, and only shared ≈ 96.1% of average nucleotide identity (ANI) with the three published T. asinigenitalis genomes, which together shared ≈ 98.3% ANI. According to current cut-offs consensus for species and subspecies delineation (95% and 98%, respectively), our results support the first insights of a sublineage delineation within the T. asinigenitalis species. • Genome of a T. asinigenitalis isolated from a Persian onager in 2018 was sequenced. • This genome (MCE663) showed atypical genetic distance from those already published. • MCE663 genome analysis suggests sublineages within the T. asinigenitalis species. [ABSTRACT FROM AUTHOR]

While different features of cell-free DNA (cfDNA) have been utilized for early cancer detection, somatic mutation has been shown to offer the highest specificity for ctDNA detection. The recent drop of sequencing cost makes it possible to track thousands of somatic variants from the cancer genomes as cancer markers in plasma, achieving high sensitivity for molecular residual disease detection. This approach, however, will be limited by errors introduced during library preparation and sequencing. Here, we describe AccuScan, a highly accurate and efficient whole genome sequencing technology that enables effective genome wide error suppression at single read level. AccuScan combines rolling cycle amplification with concatemer based error correction to remove both polymerase errors and sequencing errors. We deploy this technology in whole genome sequencing of cfDNA and demonstrated >95% sensitivity at 10-5 variant allele frequency with a specificity of 98% in an analytical study using contrived samples. AccuScan provides a high performance and scalable MRD solution that is tumor informed without personalized design. [ABSTRACT FROM AUTHOR]

We present Djerba, a software package for the translation of bioinformatic pipeline output from individual tumor genomes and transcriptomes into clinical reports for precision cancer medicine in a CAP/CLIA/ACD accredited laboratory. Specific use cases are clinical genome and transcriptome sequencing for therapeutic assignment; along with cell-free DNA sequencing using targeted panels and whole genome sequencing, for early cancer and minimal residual disease detection. The modular structure of Djerba enables it to process a wide variety of data, with reports customized for available inputs; rapid development of new reporting modes; and openness to collaboration between multiple researchers and institutions. Clinical reporting data derives from assays such as whole genome tumour/normal and whole transcriptome sequencing. Djerba inputs results from one or more bioinformatics pipelines, with tools including but not limited to GATK, VariantEffectPredictor, Sequenza, Delly, RSEM, Star-Fusion, Arriba, and MAVIS. Djerba then queries external resources such as OncoKB, for relevant clinical annotation and any recommended treatments; generates summary statistics, plots and tables with links to further information; receives a brief text summary written by a cancer genome interpretation specialist; collates its results into a machine-readable JSON document; and finally renders its output as a PDF report for use by clinicians. We upload the JSON report documents to a CouchDB database, to facilitate comparison and tracking across multiple patients. Djerba enables fast, flexible collation of genomic analysis and variant calling into a standardized, compact reporting document, in both human-readable and machine-readable formats. [ABSTRACT FROM AUTHOR]

In recent years, the global pandemic of bat-associated pathogens has led to increasing attention on bat ectoparasites. Numerous studies have identified human-associated pathogens in Nycteribiidae, indicating their potential as vectors. In this study, the first complete sequencing of the mitochondrial genome of Nycteribia allotopa Speiser, 1901 was sequenced and analyzed. We also compared the mitochondrial sequences of N. allotopa with those available in the database for other Nycteribiidae species. The complete mitochondrial genome of N. allotopa was found to be 15,161 bp in size with an A + T content of 82.49%. Nucleotide polymorphism analysis of 13 protein-coding genes from five species of Nycteribiidae showed that nad6 exhibited the most significant variation, while cox1 was the most conserved. Furthermore, selection pressure analysis revealed cox1 to exhibit the strongest purifying selection, while atp8, nad2 , nad4L , and nad5 showed slightly looser purifying selection. Pairwise genetic distances indicated that cox1 and cox2 were evolving comparatively slowly, whereas atp8 , nad2 , and nad6 were evolving comparatively quickly. Phylogenetic trees constructed using Bayesian inference and maximum likelihood methods demonstrated that all four families within the superfamily Hippoboscoidea clustered into one branch each, indicating their monophyly. N. allotopa was found to be most closely related to the same genus N. parvula. This study significantly enriches the molecular database for Nycteribiidae and provides invaluable reference data for future species identification, phylogenetic analysis, and exploration of their potential as vectors for human-associated pathogens. [Display omitted] • The mitochondrial genome of Nycteribia allotopa was sequenced for the first time. • The genome were analyzed and compared with other genome of the family Nycteribiidae. • The phylogenetic relationships of the Hippoboscoidea have been further defined. • It provides a reference for phylogeny and species identification. [ABSTRACT FROM AUTHOR]

Abstract Intraspecific variability of the behavior of most foodborne pathogens is well described and taken into account in Quantitative Microbial Risk Assessment (QMRA), but factors (strain origin, serotype, ...) explaining these differences are scarce or contradictory between studies. Nowadays, Whole Genome Sequencing (WGS) offers new opportunities to explain intraspecific variability of food pathogens, based on various recently published bioinformatics tools. The objective of this study is to get a better insight into different existing bioinformatics approaches to associate bacterial phenotype(s) and genotype(s). Therefore, a dataset of 51 L. monocytogenes strains, isolated from multiple sources (i.e. different food matrices and environments) and belonging to 17 clonal complexes (CC), were selected to represent large population diversity. Furthermore, the phenotypic variability of growth at low temperature was determined (i.e. qualitative phenotype), and the whole genomes of selected strains were sequenced. The almost exhaustive gene content, as well as the core genome SNPs based phylogenetic reconstruction, were derived from the whole sequenced genomes. A Bayesian inference method was applied to identify the branches on which the phenotype distribution evolves within sub-lineages. Two different Genome Wide Association Studies (i.e. gene- and SNP-based GWAS) were independently performed in order to link genetic mutations to the phenotype of interest. The genomic analyses presented in this study were successfully applied on the selected dataset. The Bayesian phylogenetic approach emphasized an association with "slow" growth ability at 2 °C of the lineage I, as well as CC9 of the lineage II. Moreover, both gene- and SNP-GWAS approaches displayed significant statistical associations with the tested phenotype. A list of 114 significantly associated genes, including genes already known to be involved in the cold adaption mechanism of L. monocytogenes and genes associated to mobile genetic elements (MGE), resulted from the gene-GWAS. On the other hand, a group of 184 highly associated SNPs were highlighted by SNP-GWAS, including SNPs detected in genes which were already likely involved in cold adaption; hypothetical proteins; and intergenic regions where for example promotors and regulators can be located. The successful application of combined bioinformatics approaches associating WGS-genotypes and specific phenotypes, could contribute to improve prediction of microbial behaviors in food. The implementation of this information in hazard identification and exposure assessment processes will open new possibilities to feed QMRA-models. [ABSTRACT FROM AUTHOR]

Abstract Whole genome sequencing (WGS) of important foodborne pathogens is a technology under development, but is already employed in routine surveillance by public health agencies and is being increasingly exploited in tracing transmission routes and identifying contamination events (source tracking) that take place in the farm-to-fork continuum. Furthermore, data generated from WGS, complemented by other –omics data, have the potential to be integrated into and strengthen microbiological risk assessment. In this paper, we discuss the contribution of WGS in diverse areas important to food safety and public health. Additionally, an outlook of future WGS applications, which should contribute to our understanding of the ecology and physiology of foodborne microorganisms, is presented. Highlights • Applications of whole genome sequencing (WGS) in surveillance are presented. • Suitability of WGS as a typing method for source tracking is discussed. • Potential of WGS data integration into risk assessment is evaluated. [ABSTRACT FROM AUTHOR]

Abstract Carnobacterium spp. are frequently isolated from vacuum-packaged (VP) meat. Specific strains of Carnobacterium and their growth characteristics may be associated with the storage life of such products. This study investigated the growth of 44 Carnobacterium isolates obtained from VP meat cuts produced at three Canadian abattoirs (A, B and C) under the following conditions: pH 5.4, 6.2 and 7.4; lactic acid at 60 and 90 mM; acetic acid at 33.6 mM. Whole genome sequencing was performed for all 44 isolates and a core genome phylogenetic tree was created to identify strain variability among isolates from different abattoirs. The isolates were clustered into 11 groups. All isolates from abattoirs B and C were identified as C. divergens , while the isolates from abattoir A included both C. maltaromaticum and C. divergens at equal proportions. C. divergens isolates from abattoir A belonged to two phylogenetic groups and none of them was found in the phylogenetic groups containing isolates from abattoirs B or C. Whole genome sequencing revealed that identical strains were isolated from different samples obtained at the same abattoir. The mean growth rate and maximum population density of the C. maltaromaticum isolates were lower than those of the C. divergens isolates. C. divergens isolates from abattoir A had higher growth rates and maximum population density than those from abattoirs B and C. In conclusion, growth characteristic and whole genome analysis both demonstrated strain variability of Carnobacterium among abattoirs, which could be a result of the difference in the antimicrobial interventions used for carcasses at different abattoirs, and may be associated with different storage lives of VP meats produced from different abattoirs. Highlights • Growth and whole genome sequences of 44 Carnobacterium from meat from 3 abattoirs were determined. • Carnobacterium strains varied with isolation abattoirs. • Growth behaviour of Carnobacterium spp. under meat relevant acidic conditions varied. • These variations may be related to antimicrobial interventions applied at the abattoirs. [ABSTRACT FROM AUTHOR]

Clustering pathogen sequence data is a common practice in epidemiology to gain insights into the genetic diversity and evolutionary relationships among pathogens. We can find groups of cases with a shared transmission history and common origin, as well as identifying transmission hotspots. Motivated by the experience of clustering SARS-CoV-2 cases using whole genome sequence data during the COVID-19 pandemic to aid with public health investigation, we investigated how differences in epidemiology and sampling can influence the composition of clusters that are identified. We performed genomic clustering on simulated SARS-CoV-2 outbreaks produced with different transmission rates and levels of genomic diversity, along with varying the proportion of cases sampled. In single outbreaks with a low transmission rate, decreasing the sampling fraction resulted in multiple, separate clusters being identified where intermediate cases in transmission chains are missed. Outbreaks simulated with a high transmission rate were more robust to changes in the sampling fraction and largely resulted in a single cluster that included all sampled outbreak cases. When considering multiple outbreaks in a sampled jurisdiction seeded by different introductions, low genomic diversity between introduced cases caused outbreaks to be merged into large clusters. If the transmission and sampling fraction, and diversity between introductions was low, a combination of the spurious break-up of outbreaks and the linking of closely related cases in different outbreaks resulted in clusters that may appear informative, but these did not reflect the true underlying population structure. Conversely, genomic clusters matched the true population structure when there was relatively high diversity between introductions and a high transmission rate. Differences in epidemiology and sampling can impact our ability to identify genomic clusters that describe the underlying population structure. These findings can help to guide recommendations for the use of pathogen clustering in public health investigations. • Genomic clustering of pathogens groups cases by shared transmission history. • Differences in epidemiology and sampling can influence the composition of clusters. • This impacts the utility of clustering for detecting informative groupings. [ABSTRACT FROM AUTHOR]

Novel Duck Reovirus (NDRV) that has been found throughout the world in waterfowl, and it has been extensively described. Here, we report the complete genome sequence of a NDRV strain isolated in China called NDRV YF10. This strain was collected from 87 samples with infected ducks in South Coastal Area. The NDRV genome consists of 23,419 bp. With the assistance of computer analysis, the promoter and terminator of each gene segment and 10 viral genes segments were identified, which encode polypeptides ranging from 98 to 1,294 amino acids. All gene fragments of this virus strain were determined and compared to previously reported strains, revealing genetic variation with similarity rates ranging from 96 to 99% for each gene segment. Each gene segment formed 2 host-associated groups, the waterfowl-derived reovirus and the avian-derived reovirus, except for the S1 gene segment, which was closely related to ARV evolution and formed a host-independent subcluster. This difference may be due to Avian Reovirus (ARV) evolving in a host-dependent manner. In order to evaluate the pathogenicity of YF10, a novel isolated strain of NDRV was tested in 2 types of ducks. It was observed that the YF10 isolated strain exhibits varying degrees of virulence, highlighting the potential risk posed to different types of ducks. In conclusion, our findings emphasize the importance of epidemiology studies, molecular characterization, and prevention of NDRV in waterfowl. [ABSTRACT FROM AUTHOR]

Advent of new strains and shift in predominantly circulating genotypes are characteristics of group- A rotavirus (RVA), one of the major causes of childhood gastroenteritis. During diarrheal disease surveillance at Kolkata, India (2014–2016), a shift in circulating RVA strains from G1P[8] to G3P[8] was seen. Stool samples from children (n = 3048) with acute gastroenteritis were tested of which 38.7% were RVA positive. G1 was the predominant strain (65.3%) in 2014–2015 whereas in late 2015 and 2016, G3 became the preponderant strain (44.6%). In the past decade G3 strains were not observed in this region, we conducted whole genome sequencing of representative strains to gain insight into the phenomenon of emergence and genetic constellation of these circulating human G3 strains. The analyses revealed intergenogroup reassortment in G3P[4] strains (among Wa and DS-1-like genogroup) whereas G3P[8] strains were authentic Wa-like. Phylogenetic analysis revealed Kolkata G3 strains as polymorphic and thus they formed two sub-clusters due to antigenic differences in their VP7 protein. One of the sub-clusters had the wild-type threonine at 87 amino acid position while another sub-cluster had an isoleucine mutation. Presence of additional N-linked glycosylation site at amino acid 283 of VP7 glycoprotein suggests that the major neutralizing epitope on the VP7 (G3) of RotaTeq vaccine differs from the currently circulating G3 strains. The study is important as efficiency of rotavirus vaccine depends on the circulating heterogeneous genotype constellations. Continuous monitoring of circulating RVA strains in endemic settings like India is therefore important in pre- and post-vaccination period to monitor the emergence of new reassortant genotypes in addition to assessing vaccine efficacy. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • Betaine improves coverage and stability of single cell whole genome amplification (WGA). • Measuring the presence of single copy loci across the genome serves as a proxy for WGA coverage. • Tumor clones containing novel CNVs in cancer driver loci arise during glioma growth. Abstract Uneven replication creates artifacts during whole genome amplification (WGA) that confound molecular karyotype assignment in single cells. Here, we present an improved WGA recipe that increased coverage and detection of copy number variants (CNVs) in single cells. We examined serial resections of glioblastoma (GBM) tumor from the same patient and found low-abundance clones containing CNVs in clinically relevant loci that were not observable using bulk DNA sequencing. We discovered extensive genomic variability in this class of tumor and provide a practical approach for investigating somatic mosaicism. [ABSTRACT FROM AUTHOR]

The accumulation of sequenced Francisella strains has made it increasingly apparent that the 16S rRNA gene alone is not enough to stratify the Francisella genus into precise and clinically useful classifications. Continued whole-genome sequencing of isolates will provide a larger base of knowledge for targeted approaches with broad applicability. Additionally, examination of genomic information on a case-by-case basis will help resolve outstanding questions regarding strain stratification. We report the complete genome sequence of a clinical isolate, designated here as F . novicida -like strain TCH2015, acquired from the lymph node of a 6-year-old male. Two features were atypical for F . novicida : exhibition of functional oxidase activity and additional gene content, including proposed virulence determinants. These differences, which could potentially impact virulence and clinical diagnosis, emphasize the need for more comprehensive methods to profile Francisella isolates. This study highlights the value of whole-genome sequencing, which will lead to a more robust database of environmental and clinical genomes and inform strategies to improve detection and classification of Francisella strains. [ABSTRACT FROM AUTHOR]

Background With the efficiency and the decreasing cost of next-generation sequencing, the technology is being rapidly introduced into clinical and public health laboratory practice. Aims The historical background and principles of first-, second- and third-generation sequencing are described, as are the characteristics of the most commonly used sequencing instruments. Sources Peer-reviewed literature, white papers and meeting reports. Content and implications Next-generation sequencing is a technology that could potentially replace many traditional microbiological workflows, providing clinicians and public health specialists with more actionable information than hitherto achievable. Examples of the clinical and public health uses of the technology are provided. The challenge of comparability of different sequencing platforms is discussed. Finally, the future directions of the technology integrating it with laboratory management and public health surveillance systems, and moving it towards performing sequencing directly from the clinical specimen (metagenomics), could lead to yet another fundamental transformation of clinical diagnostics and public health surveillance. [ABSTRACT FROM AUTHOR]

Objectives: Staphylococcus aureus skin and soft tissue infection (Sa-SSTI) places a significant burden on healthcare systems. New Zealand has a high incidence of Sa-SSTI, and here most morbidity is caused by a polyclonal methicillin-susceptible (MSSA) bacterial population. However, MSSA also colonise asymptomatically the cornified epithelia of approximately 20% of the population, and their divide between commensalism and pathogenicity is poorly understood. We aimed to see whether MSSA are genetically differentiated across colonisation and SSTI; and given the close interactions between people and pets, whether strains isolated from pets differ from human strains.Methods: We compared the genomes of contemporaneous colonisation and clinical MSSA isolates obtained in New Zealand from humans and pets.Results: Core and accessory genome comparisons revealed a homogeneous bacterial population across colonisation, disease, humans, and pets. The rate of MSSA colonisation in dogs was comparatively low (5.4%).Conclusions: In New Zealand, most Sa-SSTI morbidity is caused by a random sample of the colonising MSSA population, consistent with the opportunistic infection model rather than the paradigm distinguishing strains according to their pathogenicity. Thus, studies of the factors determining colonisation and immune-escape may be more beneficial than comparative virulence studies. Contact with house-hold pets may pose low zoonotic risk. [ABSTRACT FROM AUTHOR]

• This work includes a ten-year FLUBV surveillance based on WGS. • Both FLUBV lineages were detected during the study period. • Phylogenetic analyses revealed that strains belonged to different genetic groups. • Intra-lineage reassortments in PB1, PB2, NA, and NS segments were detected. • An inter-lineage reassortment in NP was observed amongst B/Vic viruses from different seasons. Influenza B viruses (FLUBV) have segmented genomes which enables the virus to evolve by segment reassortment. Since the divergence of both FLUBV lineages, B/Victoria / 2/87 (FLUBV/VIC) and B/Yamagata/16/88 (FLUBV/YAM), PB2, PB1 and HA have kept the same ancestor, while some reassortment events in the other segments have been reported worldwide. The aim of the present study was to find out reassortment episodes in FLUBV strains detected in cases attended at Hospital Universitari Vall d'Hebron and Hospital de la Santa Creu i Sant Pau (Barcelona, Spain) from 2004 to 2015 seasons. From October 2004 to May 2015, respiratory specimens were received from patients with respiratory tract infection suspicion. Influenza detection was carried out by either cell culture isolation, immunofluorescence or PCR-based assays. A RT-PCR was performed to distinguish both lineages by agarose gel electrophoresis. Whole genome amplification was performed using the universal primer set by Zhou et al. in 2012, and subsequently sequenced using Roche 454 GS Junior platform. Bioinformatic analysis was performed to characterise the sequences with B/Malaysia/2506/2007 and B/Florida/4/2006 corresponding sequences as reference of (B/VIC) and (B/YAM), respectively. A total of 118 FLUBV (75 FLUBV/VIC and 43 FLUBV/YAM), from 2004 to 2006, 2008–2011 and 2012–2015 seasons, were studied. The whole genome of 58 FLUBV/VIC and 42 FLUBV/YAM viruses was successfully amplified. Based on HA sequences, most FLUBV/VIC viruses (37; 64%) belonged to clade 1A (B/Brisbane/60/2008) except to 11 (19%), which fell within clade 1B (B/HongKong/514/2009) and 10 (17%) to B/Malaysia/2506/2004. Nine (20%) FLUBV/YAM viruses belonged to clade 2 (B/Massachusetts/02/2012), 18 (42%) to clade 3 (B/Phuket/3073/2013) and 15 (38%) fell within Florida/4/2006. Numerous intra-lineage reassortments in PB2, PB1, NA and NS were found in 2 2010–2011 viruses. An important inter-lineage reassortment event from 2008 to 2009 (11), 2010–2011 (26) and 2012–2013 (3) FLUBV/VIC (clade 1) strains to FLUBV/YAM (clade 3) was found, in addition to 1 reassortant NS in 2010–2011 B/VIC virus. Intra- and inter-lineage reassortment episodes were revealed by WGS. While PB2-PB1-HA remained in complex, NP and NS reassortant viruses were found in both lineages. Despite reassorment events are not often, the characterisation only by HA and NA sequences might be underestimating their detection. [ABSTRACT FROM AUTHOR]

Mammalian orthoreoviruses (reoviruses) are currently classified based on properties of the attachment protein, σ1. Four reovirus serotypes have been identified, three of which are represented by well-studied prototype human reovirus strains. Reoviruses contain ten segments of double-stranded RNA that encode 12 proteins and can reassort during coinfection. To understand the breadth of reovirus genetic diversity and its potential influence on reassortment, the sequence of the entire genome should be considered. While much is known about the prototype strains, a thorough analysis of all ten reovirus genome segment sequences has not previously been conducted. We analyzed phylogenetic relationships and nucleotide sequence conservation for each of the ten segments of more than 60 complete or nearly complete reovirus genome sequences, including those of the prototype strains. Using these relationships, we defined genotypes for each segment, with minimum nucleotide identities of 77–88% for most genotypes that contain several representative sequences. We applied segment genotypes to determine reovirus genome constellations, and we propose implementation of an updated reovirus genome classification system that incorporates genotype information for each segment. For most sequenced reoviruses, segments other than S1, which encodes σ1, cluster into a small number of genotypes and a limited array of genome constellations that do not differ greatly over time or based on animal host. However, a small number of reoviruses, including prototype strain Jones, have constellations in which segment genotypes differ from those of most other sequenced reoviruses. For these reoviruses, there is little evidence of reassortment with the major genotype. Future basic research studies that focus on the most genetically divergent reoviruses may provide new insights into reovirus biology. Analysis of available partial sequences and additional complete reovirus genome sequencing may also reveal reassortment biases, host preferences, or infection outcomes that are based on reovirus genotype. • Reoviruses have ten genome segments but tend to be classified based on just one. • Reovirus segment genotypes do not depend on animal host or collection year. • Most sequenced reoviruses have similar genotypes for all segments. • A few sequenced reoviruses differ in genotype for most or all segments. • There is limited evidence of reassortment among genetically divergent reoviruses. [ABSTRACT FROM AUTHOR]

Differences of sex development (DSDs) are a group of congenital conditions characterized by a discrepancy between chromosomal, gonadal, and genital sex development of an individual, with significant impact on medical, psychological and reproductive life. The genetic heterogeneity of DSDs complicates the diagnosis and almost half of the patients remains undiagnosed. In this context, chromosomal imbalances in syndromic DSD patients may help to identify new genes implicated in DSDs. In this study, we aimed at describing the burden of chromosomal imbalances including submicroscopic ones (copy number variants or CNVs) in a cohort of prenatal syndromic DSD patients, and review their role in DSDs. Our patients carried at least one pathogenic or likely pathogenic chromosomal imbalance/CNV or low-level mosaicism for aneuploidy. Almost half of the cases resulted from an unbalanced chromosomal rearrangement. Chromosome 9p/q, 4p/q, 3q and 11q anomalies were more frequently observed. Review of the literature confirmed the causative role of CNVs in DSDs, either in disruption of known DSD-causing genes (SOX9, NR0B1, NR5A1, AR, ATRX, ...) or as a tool to suspect new genes in DSDs (HOXD cluster, ADCY2, EMX2, CAMK1D, ...). Recurrent CNVs of regulatory elements without coding sequence content (i.e. duplications/deletions upstream of SOX3 or SOX9) confirm detection of CNVs as a mean to explore our non-coding genome. Thus, CNV detection remains a powerful tool to explore undiagnosed DSDs, either through routine techniques or through emerging technologies such as long-read whole genome sequencing or optical genome mapping. [ABSTRACT FROM AUTHOR]

• The study reports the presence of Spirabiliibacterium mucosae in pigeons in India. • The genome of S. mucosae TN_CUL_2021 is only the second whole genome available worldwide. • Gene luxS, biofilm forming gene has been identified specifically in S. mucosae among the members of the Spirabiliibacterium genus. Several Pasteurella like organisms isolated from various avian species were recently reclassified into new genus based on whole genome sequence analysis. One such Pasteurella like organism, Bisgaard taxon 14 was classified as Spirabiliibacterium mucosae. In the present study, a Gram-negative organism was isolated from ailing pigeons with respiratory infection from a farm in Tamil Nadu, India and the organism was misidentified as Burkholderia mallei by Vitek 2 compact system based on biochemical characterization. Since, B. mallei is highly pathogenic and zoonotic, to further confirm, 16S rDNA sequencing and analysis was carried out which revealed that the strain belonged to Bisgaard taxon 14 (Spirabiliibacterium mucosae). To further confirm the findings, whole genome sequencing of the isolate was performed. Whole genome phylogeny and average nucleotide identity (ANI) analysis showed that the genome was closely matching with Spirabiliibacterium mucosae type strain 20,609 /3. Hence, the strain from pigeon was named as Spirabiliibacterium mucosae TN_CUL_2021 and the genome was submitted in NCBI SRA database. The genome of S. mucosase TN_CUL_2021 is only the second genome available worldwide in the NCBI database. Comparative genome analysis of 26 Pasteurellaceae family strains revealed 1101 genes specific for Spirabiliibacterium mucosae. Similarly, luxS virulence gene was found only in S. mucosae and Bisgaardia hudsonensis strains. Since there are only 2 genomes available in the NCBI genome database, further studies on isolation of S. mucosae needs to be carried out to identify its epidemiology and pathogenesis so as to develop better diagnostic assays and vaccines. [ABSTRACT FROM AUTHOR]

• Whole genome sequencing of the first isolated cyanophage, LPP-1, and its relative LPP-2. • These phages belong to a group of short-tailed phages (proposed to be a new family), characterized by the ability to lysogenize their hosts. • The integration site of LPP-2 was identified, which forms the first model system to study the mechanisms and factors affecting the decision to switch between lytic and lysogenic infection in cyanophages. In the early 1960s, the first cyanophage was isolated. The description of this phage, named LPP-1, led to the extensive investigation of various cyanophages and to the study of their interactions with their cyanobacterial hosts towards controlling blooms. Here, the genomes of LPP-1 and its putative relative, LPP-2 were sequenced. Sequencing these genomes revealed that LPP-1 and LPP-2 are members of a group of short-tailed cyanophages, which are distantly related to the T7-like cyanophages. Most of the phages in this group have the ability to lysogenize their hosts. Their ability to switch between lytic and lysogenic infection may explain the formation of cyanobacterial blooms despite the persistence of their phages. This lysogenic capacity of the LPP-1-like phages occurs despite the lack of an obvious integrase gene within their genomes. Interestingly, we show that LPP-2 integrates into the host genome through an integration site in high proximity to a recombination endonuclease that may have integrase activity. Further understanding of cyanobacterial-phage relationships may provide insight into their population dynamics and suggest novel approaches for control of destructive cyanobacterial blooms. [ABSTRACT FROM AUTHOR]

1. Recognize the uncertainty inherent across the spectrum of whole genome sequencing result types. 2. Consider the challenges for pediatric palliative care teams in navigating uncertain genetic test results to inform goals of care and medical decision making. Genetic disease, including chromosomal and single gene disorders, account for substantial infant morbidity and mortality. Rapid whole genome sequencing (rWGS) combines and expands upon conventional stepwise genetic diagnostics into one rapid test, streamlining clinical diagnosis of genetic conditions. rWGS aims to inform medical decision making early in the course of care, though often yields uncertain results that confound prognostic uncertainty. Interpretation of genome results is complex, with clear pathogenic variants identified only in a minority of cases. Genome results are categorized on a spectrum from benign to pathogenic, with variant of uncertain significance (VUS) representing a grey zone. Even for pathogenic variants, there can be uncertainty regarding how they manifest in phenotypes due to factors such as penetrance and expressivity. Such uncertainty leads to significant challenges in understanding how to proceed with both nondiagnostic and diagnostic results alike. Pediatric palliative care intensively supports family-centered goals of care for neonates with potentially life-limiting genetic diseases. This case series will explore the impact of neonatal genome results on pediatric palliative care consultation: Case 1: A neonate with respiratory failure on ECMO was found to have a pathogenic variant in the FOXF1 gene consistent with the life-limiting disease alveolar capillary dysplasia with misalignment of the pulmonary veins, prompting transition to comfort measures. Case 2: A neonate with intractable epilepsy and structural brain abnormality was found to have a likely pathogenic variant in the NPRL3 gene. Genome results impacted medical decision making, including trial of a new medication and limitation of surgical interventions with discharge home on hospice. Case 3: An infant with congenital hypotonia and episodic metabolic crises and clinical decompensation was diagnosed with a VUS in the AIFM1 gene revealing a potential relevant mitochondrial disease. Given the infant's ongoing clinical decompensation, the genetic results informed shared decisions to limit interventions including intubation and resuscitation. [ABSTRACT FROM AUTHOR]

Pasteurella multocida ( P. multocida ) is a zoonotic bacterium that can cause diseases in a variety of animals. It was divided into 5 serogroups, and serogroup A is mainly prevalent in avian hosts. We isolated a virulent and multidrug-resistant P. multocida strain from Guangdong duck liver and named it PMWSG-4 (GenBank accession no. CP077723.1). To understand the pathogenicity of this strain, the pathogenicity test was carried out with mice and ducks. The results showed that PMSWG-4 was highly pathogenic to ducks and mice, and the LD50 is 4.5 and 73 CFU, respectively. In order to study its genetic characteristics, pathogenicity, and relationship with the host, we performed a whole genome sequencing. The genome size of the isolated PMWSG-4 was 2.38 Mbp, with a G+C content of 40.3%, and coding 2,313 Coding DNA Sequence (CDS). The genome carries 162 potential virulence-associated genes, 32 different drug resistance phenotypes, 102 genes possibly involved in pathogen–host interaction, 2 gene island groups, and 4 prophages. In addition, we also found a new drug-resistant plasmid from strain PMWSG-4, named pXL001 (GenBank accession no. CP077724.1). After verified, the plasmid is a new plasmid carrying the floR florfenicol resistance gene. The whole genome is of great significance for further studying the pathogenesis and genetic characteristics of duck-derived P. multocida. [ABSTRACT FROM AUTHOR]

Kosta goat is one of the Indonesian local goats which had the potential to utilize, while their genetics was not yet characterized. Since, a high mutation of Mitochondria DNA (mtDNA), it is widely applied to understand species evolutionary, phylogenetic, and characterized population genetics. Whole genome sequencing of Mitochondria DNA has new insight to elucidate genetic characteristic of goat completely. Therefore, this study purposes to explore the whole mitochondrial DNA of the Kosta goat and its relationship with other breeds based on Whole Genome Sequensing (WGS). The Kosta goat mitochondria genome was collected from whole blood, which was enriched using REPLI-g Mitochondrial DNA Kit (Qiagen). Oxford Nanopore Technology was employed in the mtDNA sequencing. The assembled sequence was polished with Racon and Medaka , and was further determined using Quast. Furthermore, Annotation and Visualization were conducted using MitoZ and Mitos Webserver. The sequence mitochondria genome of the Kosta goat has 16,641 bp, consisting of 13 PCGs (Protein Coding Genes), 22 tRNA, 2 rRNA, D_loop region, as well as OL (origin loop) sequences. Also, it has a base composition of 33.57 % for Adenin (A), 27.31 % for Timin (T), 26.04 % for Cytosin (C), and 13.08 % for Guanin (G), with sequential percentages of A>T>C>G. The start codons of PGCs are primarily initiated by ATG, whereas for ND2, ND3, and ND5 by ATA. Specific genetic characteristic of mitogenome Kosta goat has 309 bp length of ND3. Kosta goat belongs to Lineage B, and this follows the study of other Indonesian goats. Complete mitochondrial DNA of Kosta goats can be used to characterize their genetic potential, genetic diversity, phylogenetic analysis to support their utilization and conservation. • Kosta goat is one of Indonesian local goats. • Complete Mitochondrial DNA sequencing is a new insight to elucidate genetic characteristic of Kosta goats. • Complete mitochondrial DNA of Kosta goat may help provide data for further analysis on the mtDNA sequence to support goat genetic research. [ABSTRACT FROM AUTHOR]

Whole genome sequencing (WGS) can help to relate Mycobacterium tuberculosis genomes to one another to assess genetic relatedness and infer the likelihood of transmission between cases. The same sequence data are now increasingly being used to predict drug resistance and susceptibility. Controlling the spread of tuberculosis and providing patients with the correct treatment are central to the World Health Organization's target to ‘End TB’ by 2035, for which the global prevalence of drug-resistant tuberculosis remains one of the main obstacles to success. So far, WGS has been applied largely to drug-susceptible strains for the purposes of understanding transmission, leaving a number of analytical considerations before transferring what has been learnt from drug-susceptible disease to drug-resistant tuberculosis. We discuss these potential problems here, alongside some of the challenges to characterizing the Mycobacterium tuberculosis ‘resistome’—the optimal knowledge-base required for WGS-based assays to successfully direct individualized treatment regimens through the prediction of drug resistance and susceptibility in the future. [ABSTRACT FROM AUTHOR]

Catfish (Siluriformes) are one of the most diverse vertebrate orders and are characterized by whisker-like barbels, which are important sensory organs in most of teleosts. However, their specific biological functions are still unclear. Red-tail catfish (Hemibagrus wyckioides) is well-known catfish species with four pairs of barbels, of which the maxillary barbels reach two-thirds of the body length. In this study, a 776.58 Mb high-quality chromosome-level genome was assembled into 29 chromosomes. Comparative genome data indicated that the barbeled regeneration gene ccl33 has expanded into 11 tandemly duplicated copies. Transcriptome data revealed the functional differentiation of different barbels and suggested that the maxillary barbel might be necessary for water temperature perception. Taste receptor genes were also characterized in teleosts with different food habits. Selection pressures were revealed to affect the sugar-based solute transport domain of the sweet taste receptor gene t1r2 in carnivorous fishes. In addition, the bitter taste receptor gene t2r200 was found to be lost from the genomes of four catfish species. Therefore, our study provides a genomic foundation for understanding the regeneration and functional differentiation of barbels in red-tail catfish and also reveals novel insights into the feeding evolution of fish species with different feeding habits. • A high-quality reference genome sequence with complete annotation in red-tail catfish was assembled in this study. • Genome evolution among the different catfish genomes was explored. • Barbeled regeneration gene ccl33 was found to be tandemly duplicated in red-tail catfish genome. • This research revealed functional differentiation of four pairs of barbels. • Two taste receptor genes t1r2 and t2r were characterized in different food habit teleosts. [ABSTRACT FROM AUTHOR]